Description Usage Arguments Value Examples
Retrieve alignments with attendant pulse features.
1 2 | getAlignmentsWithFeatures(cmpH5, idx = 1:nrow(cmpH5),
fxs = getIPD, collapse = FALSE)
|
cmpH5 |
An object of class |
fxs |
A list with functions of the form |
idx |
The indices of the alignments to return. |
collapse |
Whether a list of data.frames should be returned or a single data.frame with a column naming the alignment. |
Either a list of data.frames or a data.frame
1 2 3 4 5 6 7 8 9 10 | require(pbh5)
cmpH5 <- PacBioCmpH5(system.file("h5_files", "aligned_reads.cmp.h5",
package = "pbh5"))
alnsPlusFeatures <- getAlignmentsWithFeatures(cmpH5,
fxs = c("IPD" = getIPD,"PulseWidth"=getPulseWidth), idx = 1, collapse = TRUE)
head(alnsPlusFeatures)
boxplot(IPD ~ reference, data = alnsPlusFeatures, log = 'y',
ylim = c(.05, 10), main = "Distribution of IPDs Conditioned on Base")
plot(density(log(alnsPlusFeatures$PulseWidth), na.rm = TRUE), main =
"Distribution of Global Pulsewidth")
|
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